Is the doctor a neurologist? If not, do you expect to the doctor to refer your sister to a neurologist? Initially I saw a G.P., then three neurologists, and a G.P. who focused on alternative medicine. In each case, I was usually overwhelmed with information - more answers than I had questions for. Your sister will need time to sort through the info.
In each case, the neurologist recommends a treatment, usually one of the currently approved M.S. drugs. They'll usually provide you with all sorts of imformation on these drugs, everything from videos (vhs), 800 support numbers, to a nurse specifically trained in the treatments.
From there, I guess it is a matter of deciding which treatment plan your sister and her doctor feel is the best for her. If your sister decides that she would prefer a different treatment, then she might ask the doctor what other options are available.
Have you been to the site Remedy Find? At that site patients rate their experience/effectiveness of various treatments. Otherwise, I think you'll find this site one of your greatest resources for information. However, with regard to questions, I think questions will depend upon the treatment plan your sister chooses and how flexible or open the doctor is.
If you review the material posted on this site, you might find that your sister will be interested in options other than the currently approved M.S. treatments. If so, she may want to ask the doctor how he feels about these various treatments.
Unfortunately, there are no routine/suggested questions because there are so many variants. Often you'll find that the doctors cannot even answer the questions because there's so much they simply don't know. In fact, some of the alternative therapies have information available for the patient to share with their doctor.
Best wishes to your sister and your family as you endure this maze of information, make decisions, and supprt her.